Exam 1 (Exam 1&2&Final Comp)

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Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA

GLMK TYPDSTA

A solution of which of the following would be a good buffer system? A) CH3COOH and NaCH3COO B) HCl and H2O C) NaOH and KOH D) none of the above E) HCl and NaOH

Given a biological system at 1 atm with 16kJ/g, what is the internal energy of the system? A) 16kJ/g B) not enough information is given to calculate the answer C) 15kJ/g D) 14 kJ/g

How many beta turns or beta loops are required to construct a beta sheet composed of four antiparallel strands? A) 3 B) 4 C) 6 D) 0 E) 5

Which amino acid side chain from the list below is the most polar?

Gln

beers law relations

*a small change (decrease) in I takes place over a small path length, dL, at given concentration. log(I0/I) =ecl = A (unitless)

exopeptidace

*cuts C terminal AA *cuts N terminal AA

molten globule

*inside forms first

14. Which of the following is an example of a polysaccharide?

Glycogen

Using the actual reduction potential that you calculated in question #4, what is the new calculated overall change in standard free energy for the isocitrate dehydrogenase reaction from question #3 and is it more or less favorable under these actual conditions?

-19.3 kJ/mol, more favorable

1. Which of the following steps used to convert solar energy to chemical energy does NOT involve the movement of electrons?

ATP synthesis by the chloroplast ATP synthase complex

A patient is having problems regulating blood pressure and has poor kidney function. Which steroid could be responsible for this? progesterone cortisol aldosterone estradiol

aldosterone

R group charged at pH of 12

asp

charged amino acids

asp, glu, lys, arg, his

An oxygen binding curve of fractional saturation versus pO2 displays a sigmoidal shape. This is the oxygen binding curve for

hemoglobin in the presence of 2,3-bpg

Which of the following pathways are found in both plants and animals?

citrate cycle

what drives hydrophobic collapse

increase in delta S fold

If a typical person hydrolyzes 100.0 mol of ATP per day, how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol.)

50.7kg

When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme?

Reverse transcriptase

Enzyme active sites are nonspecific. are a pocket or cleft. always exclude water. can only bind a single substrate at a time.

are a pocket or cleft.

Calculate the DeltaEo' of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table below.

1.25

Calculate the mc017-1.jpg of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table below. mc017-2.jpg

1.25

hydrogen bonding in tertiary protein

During intense exercise, muscle ATP stores will be depleted in about 3 minutes. 5 minutes. 30 seconds. 3 seconds.

3 seconds

How many different forms of pyridoxal phosphate are observed in the aminotransferase reaction? 7 6 5 4

What would be the expected orientation of an amphipathic alpha helix occurring in a globular protein in aqueous solution?

A soluble protein will have lots of hydrophilic amino acids on its surface, so the helix will be arranged to have the hydrophilic side facing toward the outside of the protein.

What is the appropriate order of the following steps? A. Glutamine binding to uridylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase

A, C, B

The citrate cycle is often called the metabolic engine in the cell. IN this analogy, what is considered the work, the fuel, and the exhaust?

ATP synthesis, acetyl CoA, CO2

The sequencing of the human genome has been instrumental toward

All of these areas were enhanced by the sequencing of the human genome

For the alanine titration curve shown below, which best describes point A?

An isoelectric point

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

CCNC

What side products of pyruvate are being converted into alcohol and carbon dioxide by yeast?

CO2 and NAD+

9. Photons first enter the Z scheme via which molecule?

Chlorophyll P680

22. Which of the following cellular structures is NOT involved in the glyoxylate cycle?

Chloroplast

Which metabolite is an allosteric activator of the enzyme acetyl-CoA carboxylase? A. Glucose B. Glycerol-3-phosphate C. Acetyl-CoA D. Citrate E. NADH

Citrate

The drug oligomycin inhibits ATP synthase by preventing protons from flowing through the enzyme. Oligomycin must bind to the __________ of ATP synthase.

Fo subunit of

What is the "cost" of using the glycerol-3-phosphate shuttle instead of the malate-aspartate shuttle in terms of proton-motive force and ATP synthesis? (choose one correct answer).

For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis

Which of the following is a GTPase?

Gsa

order the following according to hierarchal placement a desert b lizard c hexokinase d muscle cell F fructose g glycolysis h hydroxyl group i earth

H, F, C, G, D, B, A, I

The chirality of naturally occurring amino acids in proteins is

counter clockwise rotation

L Left (levorotary)

If SERCA is not functioning in a myoblast, which of the processes described at the right is most likely to occur?

Muscle contraction occurs but not muscle relaxation

What would happen if DNA contained uracil isntead of thymine as the adenine base pair?

Naturally ocuring uracil bases would not be distinguishable from cytosine deamination events

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called

Operons

How does the O2-evolving complex (OEC) link the oxidation of H2O with the restoration of P680?

The four electrons formed from the oxidation of H2O to O2 in the PSII are held by a Mn4 cluster in the OEC. For every P680 chlorophyll molecule that is photooxidized, one electron from the OEC is used to reduce P680+.

Why is the process of purifying proteins from cells considered challenging?

There are 10,000 to 100,000 proteins in one sample

Which of the following is correct about topoisomerases?

Type II topoisomerases reduce positive supercoiling generated during replication or transcription

What are the three-letter and one-letter abbreviations for the amino acid tyrosine?

Tyr, Y

The graph below shows the relative changes in concentration of glucose, fatty acids, and ketone bodies during 40 days of starvation. Choose the answer that correctly labels the data on the graph. X = fatty acids; Y = glucose; Z = ketone bodies X = glucose; Y = fatty acids; Z = ketone bodies X = ketone bodies; Y = glucose; Z = fatty acids X = ketone bodies; Y = fatty acids; Z = glucose

X = ketone bodies; Y = glucose; Z = fatty acids

What is the dominant secondary structure found in hair keratin?

alpha helices

A hydrogen bond can best be described as a

weak noncovalent interaction

Which of the following biochemical relationships are CORRECT statements illustrating the hierarchical organization of molecular life? Choose the THREE best answers.

(1) Carbon, hydrogen and oxygen are the most abundant elements in biomolecules. (2) Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems (3) Insects degrade organic materials on the forest floor and generate nitrogen compounds used by the tree seedlings as nutrients

identify the three conditions in the list below that best describe low energy charge in a cell

- low atp concentration -energy charge rate below 0.70 -high AMP concentrations

Although most protein sequencing is now done by mass spectrometry (MS), Edman degradation (ED) is useful if large amounts of a protein can be obtained even if from an uncharacterized species. Answer the True/False questions regarding methods used to sequence a polypeptide fragment and choose the set of all correct answers. 1. True / False - The N-terminal residue removed by acid treatment in ED is always a methionine. 2. True / False - Trypsin and chymotrypsin treatment often provides identical peptide fragments for ED. 3. True / False - Genomic sequences are needed to predict protein sequences by the MS method. 4. True / False - Trypsin treatment provides useful sequence information when analyzing data from MS. 5. True / False - Protein sequencing by ED does not require purified protein but sequencing by MS does.

(1) False (2) False (3) True (4) True (5) False

Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE?

(1) Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. (2) The majority of autotrophs on Earth require aerobic respiration in order to survive. (3) Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration.

Name the four noncovalent interactions that occur within and between biomolecules that facilitate life processes at the molecular level. Which of these noncovalent interactions directly or indirectly involve H2O molecules? (ch.2)

(1) Hydrogen bonds, (2) ionic interactions, (3) van der Waals interactions, and (4) hydrophobic effects. Hydrogen bonds form directly between H2O and biomolecules and between H2O molecules themselves, whereas hydrophobic effects are indirectly caused by H2O due to "water-avoiding" interactions between nonpolar molecules.

Answer the following questions about the graph shown above and record the set of answers in the correct order. 1. The protein with the lowest dissociation constant (Kd) is protein (A or B)? 2. The protein with the highest affinity for oxygen is protein (A or B)? 3. The protein most likely to bind oxygen cooperatively is protein (A or B)? 4. The protein most likely to be an oxygen storage protein is protein (A or B)? 5. The protein most likely to be hemoglobin is protein (A or B)? 6. The protein most likely to be myoglobin is protein (A or B)?

(1) protein A (2) protein A (3) protein B (4) protein A (5) protein B (6) protein A

Predict the structure of a fatty acid that is trans 16:1 (delta^9).

(there's another option where the double bond is on the other side, don't pick that one)

christian anfunsin

*1957 1. RNase treated with urea and pME resulted in primary structure(single chain of AAs) 2. then added O2 which reestablished disulfide bridges but not activity. 3. after adding O2 then dialysis of urea it resulted in 90% of activity regained.

alpha helical stability

*25% of globular proteins contain alpha-helices 3 components: 1.H-bonding between j and j+4 2. R groups point away from helical axis 3. electrostatic interactions between R groups

tetromer

*4 subunits *noncovalently assembled

Hemoglobin

*Hb *Hb~4Mb *both Hb and Mb contain an iron 2+ heme *Hb has 2 different protomers, *Hb consist of a homodiner and heterodimer

for molecular weight determination, use SDS page

*SDS- sodium dodeacylsulfate CH3-(CH2)11-O-SO3- *sulfur binds to charged groups. *hydrophobic end - causes the protein to denature-unfold. *unfolded protein binds SFS ~1.4 gsds/g of protein *SO3- gives overal negative to the denatured protein *SDS destroys tertiary and quaternary structures.

sequencing proteins

*Why: sequence >> function (folding) *x-ray could be used for sequencing *some proteins don't form crystals *there are regions of disorder(N.C terminus) *a single site mutation (SNP) can cause disease.

sequencing by edman

*a limited hydrolysis/dragging that gives that N-term residue, N+1 residue >> N 1. form an edman reagent adduct (+ag) 2. cleavage of N-term +agged AA

beta-sheet structures

*allows for adjacent amino acid residues (backbones) to Hbond *pleated sheet is held together by Hb between residues (across) *residues up/down in staggard fashion

quartenary structure

*an arrangement of protein subunits *examples: Myoglobin(Mb - oxygen storage), Hemoglobin(Hb -oxygen transport)

electrophoresis

*electric field used to separate proteins (DNA/RNA) based on their molecular weight. *The force on anion due to an electric field. *F= qE

chyinstrysin

*endopeptide *cuts only at aromatic residues except when the proceeding AA is Pro.

chaperone proteins

*help protein under stress maintain its conformation *heat shock proteins *cold shock proteins *ATPases to bind a nacscient protein next to the ribosome, and help it fold to its adult shape away from destabilizing factors.

two kinds of interactions to form oligomers

*homologous>>>isologous *heterologous

protein source for protein purification

*large quantities of hearts, kidneys *crush tissue *break cells *large scale chemical extraction based on fundamental chemical characteristics.

primary protein structure definition

*linear sequence of AA that make of the protein monomer

column chromatography

*load resin into column... elute *wash non-binding proteins *SDS page to check punity.

antiparallel beta sheet

*most common *2 stranded beta sheet *arrow always points toward C terminal *amino acid residues are much further apart.... less dense than alpha helix

quaternary protein structure definiton

*multimers(dimers, trimers..) form a large non-covalently bound proteins. *sometimes nature uses -S-S- disulfide bonds to covalently connect monomers

SDS page

*polyacrylamide gel electrophoresis *acrylamide is polymorized using cross linking. *page only(no SDS detergent) -separation of amino acids

secondary protein structure definition

*polypeptides from 4-20+ AAs that form common motifs. (motifs: alpha-helix, beta sheets)

size elcusion chromatography

*separates molecules by size *the stationary phase contains cross-linked polymers with different pore sizes. *uses a mobile phase and a stationary phase to separate proteins.

statements describing SDS page

*sodium dodecyl sulfate denatures the proteins and adds negative charge, resulting in protein separation by size only. *sds page uses a polyacrylamide gel to separate proteins. *smaller proteins migrate farther than larger proteins.

lambert beer law of optical absorption

*the absorption of a particular wavelength of light by a molecule(in solution) depends on the concentration of the solution, the path length(l or b, units in cm) and E . *E=molar decaadic coefficient *E is a quantum mechanical property of the molecule. *E is the optical absorption spectrum *E=E(wavelength)

biomolecules that have color

*visible, UV, IR *bees see in UV (chromophore) *snakes can "see" in the infared IR (chromophore)

Which of the following are properties of water? A. Water is less dense as a solid than as a liquid. B. Water is liquid over a wide range of temperatures. C. Water is miscible with oil. D. Water is a strong acid at high temperatures. E. Water is polar and an excellent solvent because of its hydrogen-bonding properties. F. Water freezes more readily when ionic solutes are dissolved in it.

A, B, and E

Which of the following are mechanisms of horizontal gene transfer that can insert DNA into a bacterial cell? A. transformation B. transcription C. transduction D. conjugation

A, C, and D

Which of the following is an example of a weak acid? Choose one: A. Vinegar, CH3COOH B. HCl C. Ammonia, NH3 D. NaOH

A- Vinegar, CH3COOH

The mobility of lipids in membranes is best described by Choose one: A. fast lateral diffusion and slow transverse diffusion. B. slow lateral diffusion and fast transverse diffusion. C. slow lateral diffusion and slow transverse diffusion. D. fast lateral diffusion and fast transverse diffusion.

A- fast lateral diffusion and slow transverse diffusion

Which of the following types of chromatin is usually associated with non-coding DNA? Choose one: A. heterochromatin B. euchromatin

A- heterochromatin

For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change?Choose one: A. The EC would increase. B. The EC would remain unchanged. C. There is no way to predict how the EC would change. D. The EC would decrease.

A- the EC would increase

Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur? Choose one or more: A. The unfavorable reaction is coupled to a favorable one. B. Energy is absorbed from the surroundings. C. A favorable enthalpy change overcomes entropic penalty. D. It is not possible.

A- the unfavorable reaction is coupled to a favorable one C- A favorable enthalpy change overcomes entropic penalty

If a cell is placed in a hypotonic solution, thenChoose one: A. water will flow into the cell. B. water will flow out of the cell. C. there will be no net change in flow of water into or out of the cell. D. solutes in the solution will enter the cell.

A- water will flow into the cell

Which of the following three terms includes the other two? A) homologous B) orthologous C) paralogous

A-homologous

When a protein enzyme folds in an aqueous solution, which of the following is correct? Choose one: A. Non-polar amino acids are found in the interior of the protein. B. Polar amino acids are found in the interior of the protein. C. A mixture of polar and non-polar amino acids is found in the interior of the protein. D. Water is always excluded from the active site in the interior of the protein.

A-nonpolar amino acids are found in the interior of the protein

Consider the following DNA: 5'-AGGCT-3'. If this were serving as the template strand for new polynucleotide polymerization, how would the new strand read? Choose one: A. 3'-TCCGA-5' B. 3'-AGGCT-5' C. 5'-TCCGA-3' D. 5'-AGGCT-3'

A. 3'-TCCGA-5'

DNA methylase enzymes transfer a methyl group to C-5 of a cytosine or to N-6 of an adenine within a DNA sequence recognized by the enzyme. What effect, if any, would this have on the establishment of the HindIII-DNA complex that is shown in this molecular structure? Choose one: A. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. B. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. C. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site. D. If the HindIII target DNA were methylated, then it would not alter the probability of binding between HindIII and DNA and would not alter the endonuclease activity at that methylated site. E. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site.

A. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site.

Which of the following is expected for DNA that is exposed to increasingly elevated temperature? Choose one or more: A. The quantity of light absorbed at wavelength 260nm is expected to increase. B. The quantity of light absorbed at wavelength 260nm is expected to decrease. C. The quantity of light absorbed at wavelength 260nm is expected to remain constant. D. The sample is expected to behave more like DNA with intact base pairs. E. The sample is expected to behave more like DNA with disrupted base pairs.

A. The quantity of light absorbed at wavelength 260nm is expected to increase. E. The sample is expected to behave more like DNA with disrupted base pairs.

How much space along the longitudinal axis of DNA does the HindIII enzyme occupy when bound? Choose one: A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms B. approximately two major grooves and the two neighboring minor grooves, which in total is approximately 40 angstroms C. approximately three major grooves and the three neighboring minor grooves, which in total is approximately 20 angstroms D. approximately four major grooves and the four neighboring minor grooves, which in total is approximately 20 angstroms

A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms

Which of the following gene expression assays requires that the sequence of genes be known in advance? Choose one: A. gene microarray B. RNA-seq analysis C. both RNA-seq analysis and gene microarray D. neither RNA-seq analysis nor gene microarray

A. gene microarray

The excess sodium ions are most likely interacting with which chemical component of the nucleotides? Choose one: A. phosphate group B. nitrogenous base C. pentose sugar

A. phosphate group

the carbon nitrogen peptide bond is rigid. A.which of the following most likely describes part of an observed alpha helix B. which of the following would NOT likely occur in a beta sheet?

A. psi = -60degrees; psi=-47degrees, many ala residues B. psi=+60;psi=+60, many gly residues psi=-57;psi=-49, many ala residues psi=-51; psi=+153, many gly and pro residues.

Chargaff's rule is that the amount of

A=T and the amount of C=G

Within one of the homodimeric Fe protein components, shown in green, which ligand has a binding site within each part of the dimer? Choose one: A. ADP B. P cluster C. 4 Fe-4 S cluster D. FeMo cofactor

ADP

Which of the following molecules would activate phosphofructokinase 1 (PFK1)? NADH AMP ATP pyruvate

AMP

helix making, stabilizing

ARG+_______-GLU (salt bridge) pi-stacking

Which of the following statements are true?

ATCase is regulated by feedback inhibition

A high concentration of which molecule would inhibit citrate synthase in the citrate cycle?

ATP

To study the allosteric regulation of E. coli ribonucleotide reductase in a cell-free in vitro system, which of the following would be a good choice to add to the system? glucose ATP Ca2+ IP3

ATP

Which of the following molecules would inhibit the last reaction of glycolysis? ATP glucose AMP NAD+

ATP

What precursors are required for the breakdown of palmitate? 14 ATP and 14 NADH ATP and CoA acetyl-CoA NADH and FADH2

ATP and CoA

11. Among the Calvin cycle inputs, which ones are generated by the light reactions of photosynthesis?

ATP and NADPH

The Calvin cycle requires which species from the light reactions? ATP and NADPH reducing electrons CO2 and ATP NADH and FADH2

ATP and NADPH

Phosphorylation of serine residues is a common way to regulate the activity of proteins. The source of phosphate for phosphorylation is ATP. Here are the two reactions involved: phosphoserine + H20 <==> serine + Pi ΔG°' = -10.3 kJ/mol ATP + H2O <==> ADP + Pi ΔG°' = -30.5 kJ/mol Using the information in the reactions above, which of the following are correct?

ATP hydrolysis is exergonic

ATP synthesis rates will decrease because of decrease of the proton-motive force. O2 consumption will decrease after the addition of carbon monoxide, because O2 will not be reduced by the ETS.

Given the following common reactions, which are entropically favored?

ATP ⇒ ADP + Pi

What is the net reaction (1+2) shown below (???) and what is the delta G (???) for this net reaction?

ATP+Glutamate+NH4+ <-> Glutamine+ADP+Pi G=-16.3 kJ/mol

The step in solid-phase peptide synthesis that occurs at number 2 is

Activation of the Fmoc blocked residue

Associate each cellular condition or molecular state with its effect on the Calvin cycle.

Active Calvin Cycle NADP+ becomes limiting in the stroma. Ferredoxin continues to donate electrons to ferredoxin-thioredoxin reductase at night. Inhibited Calvin Cycle Chloroplast thioredoxin gene is unable to be expressed. Mutant version of ferredoxin-thioredoxin reductase irreversibly binds thioredoxin.

Below shows the cell survival pathway promoted by TNF-mc171-1.jpg. A complex is indicated with a question mark. What is this complex?

Active NFkB

Consider the pathway A → B → C → D → E. Reactions A → B, B → C, and D → E have a ΔG near equilibrium, while C → D has a ΔG << 0. Which of the following is true about this pathway if it were operating within a cell?

Adding more A to the system will increase the amount of B and C in the system.

Which of the following enzymes from glycolysis does NOT have an equivalent enzyme involved in stage 2 of the Calvin cycle?

Aldolase

Observe only the seven fatty acid ligands of serum albumin. Which of the following is correct for this specific example?

All seven of these ligands contain an unsaturated hydrocarbon chain.

Which two functional groups are involved in producing a peptide bond?

Amino and carboxyl

What two functional groups are found in producing a peptide bond?

Amino and carboxyl groups

Select the TWO true statements about amphipathic alpha helices from the statements below. For a membrane protein with a single membrane spanning alpha helix, this helix is often amphipathic. Amphipathic alpha helices are charged on one face and polar on the other. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. It is energetically favorable for an amphipathic alpha helix to be completely buried in the hydrophobic core of a protein. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. A polypeptide sequence with alternating polar and nonpolar residues (P-N-P-N-P-N etc) will form an amphipathic alpha helix. Amphipathic alpha helices are most often found transversing the plasma membrane as components of GPCRs.

Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein.

Select the THREE true statements about amphipathic alpha helices from the statements below. Amphipathic alpha helices are charged on one face and polar on the other. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. For a membrane protein with a single membrane spanning alpha helix, this helix is often amphipathic. An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. It is energetically favorable for an amphipathic alpha helix to be completely buried in the hydrophobic core of a protein. Amphipathic alpha helices are most often found transversing the plasma membrane as components of GPCRs. A polypeptide sequence with alternating polar and nonpolar residues (P-N-P-N-P-N etc) will form an amphipathic alpha helix.

Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein.

Again consider the pathway above. Under what conditions would adding more A to the system not lead to an increase in the flux of the pathway from A to E?

An allosteric inhibitor of the enzyme that catalyzes C → D is also present in the system. The enzyme that catalyzes C → D has already reached 100% of Vmax.

Describe the properties of an amphipathic alpha helix and identify numbered amino acids in a dodecamer polypeptide that contribute to the chemical properties of this secondary protein structure. Where are amphipathic alpha helices found in a globular cytosolic protein?

An amphipathic alpha helix has a hydrophobic face and a hydrophilic face owing to the arrangement of hydrophobic and hydrophilic side chains in the sequential amino acids. A dodecamer would have hydrophobic residues at positions 2, 3, 5, 6, 9, and hydrophilic residues at positions 1, 4, 7, 11, 12. Amphipathic alpha helices are found on the surface of globular cytosolic proteins

Select the THREE true statements about amphipathic alpha helices from the statements below.

An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face.

Which of the following would be an example of decreasing entropy?

An anabolic pathway

Evaluate which of the following statements is/are true about enzymes and the transition from reactants to products.

An enzyme does not change the energy of the reactants or product, nor does it change the equilibrium constant of a reaction. An enzyme lowers the activation energy of a reaction, which means the transition state is not as energetically unfavorable as it would be without the presence of an enzyme.

topoisomerase

An enzyme that catalyzes the cleavage of one or both DNA strands and relaxes positive supercoiled regions, allowing DNA to return to its relaxed state. (p. 103)

restriction endonuclease

An enzyme that cleaves DNA at specific sequences; isolated from bacteria that use restriction endonucleases to protect against invading bacteriophage. (p. 130)

Binding of the negatively charge allosteric effector 2,3-bisphosphoglycerate (2,3-BPG) stabilizes the T state of hemoglobin. A lysine residue in the central cavity of hemoglobin interacts with 2,3-BPG. In a hemoglobin variant, there is a substitution of this lysine by an asparagine. Relative to the wild-type hemoglobin, this variant would be expected to have. Choose the ONE most correct statement. An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG An increased affinity for oxygen in the presence of 2,3-BPG, and a decreased affinity in the absence of 2,3-BPG An equivalent affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG

An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG

What is the biochemical explanation for the observed toxic effects of arsenic contaminated well water in Bangladesh? There are TWO correct answers. Arsenic is converted to arsenite, which covalently modifies reduced lipoamide, thereby inhibiting activity of the pyruvate dehydrogenase complex and blocking conversion of pyruvate to acetyl-CoA. Cracked skin on the feet is caused by aresenic crystals deposited in the keratin granules of the lower extremities, and once they form, the only treatment is daily application of acai beri beri extract. TPP and arsenic form an inactive vitamin complex called B12 that scavenges acetyl-CoA from the citrate cycle causing low energy charge and eventual apoptosis. The aresenic contaminated well water caused inhibition of dihydrolipoyl transacetylase, which is an enzyme subunit required for metabolism of rice starch, the source of 70% of their daily caloric intake. Aresenite activates thiaminase in the small intestine, which decreases functional levels of thiamin required to produce TPP, resulting in dangerously low levels of vitamin D and riboflavin. Arsenite froms a bidentate adduct on oxidized dihydrolipoamide and this blocks conversion of pyruvate to oxaloacetate, thereby inhibiting flux through the citrate cycle. Two correct answers are not provided. Arsenic is an electron carrier that accepts electrons from thiamin pyrophosphate and thereby short circuits the dihydrolipoamide transacetylase reaction by donating electrons directly to FAD.

Arsenic is converted to arsenite, which covalently modifies reduced lipoamide, thereby inhibiting activity of the pyruvate dehydrogenase complex and blocking conversion of pyruvate to acetyl-CoA. the aresenic contaminated well water caused inhibition of dihydrolipoyl transacetylase, which is an enzyme subunit required for metabolism of rice starch, the source of 70% of their daily caloric intake.

Which of the THREE following statements about the charge on the pentapeptide AHDLV at pH 2, pH 7, and pH 10 are correct? Use the following table of pKa values to solve the problem. Chemical group: pKa terminal a-carboxyl: 3.1 sidechain carboxyl: 4.1 imidazole: 6.0 terminal a-amino: 8.0 thiol: 8.3 aromatic hydroxyl: 10.9 e-amino: 10.8 guanidino: 12.5 Possible Answers: At pH 7, the charge on the peptide is -2. At pH 2, the charge on the peptide is -1. At pH 7, the charge on the peptide is -1. At pH 10, the charge on the peptide is zero. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

At pH 7, the charge on the peptide is -1. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

Which of the THREE following statements about the charge on the pentapeptide AHDLV are correct? Use the following table of pKa values to solve the problem. Chemical group pKa terminal a-carboxyl 3.1 sidechain carboxyl 4.1 imidazole 6.0 terminal a-amino 8.0 thiol 8.3 aromatic hydroxyl 10.9 e-amino 10.8 guanidino 12.5

At pH 7, the charge on the peptide is -1. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

Calculate the pH of a solution containing 0.105 M HA and 0.146 M A-. The Ka for the weak acid is 1.8x10^-5 A) 7 B) 4.88 C) 9.11 D) 2.44 E) 4.74

For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change? A. The EC would remain unchanged. B. The EC would increase. C. There is no way to predict how the EC would change. D. The EC would decrease.

Given the energy charge equation, if a biological system has an EC=0.8, what is true about the concentrations of ATP, ADP, and AMP in the system? A) the concentrations are all equal B) there is more ATP in the system than ADP or AMP C) There is more ADP in the system than ATP or AMP D) none of the above E) There is more AMP in the system than ATP and ADP

If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water? A. The protein would demonstrate no change in water binding. B. The protein would not bind water and would lose antifreeze properties. C. The protein would bind water more tightly. D. The protein would have increased affinity for the phosphate backbone of DNA.

RNA-seq is considered to be complementary to gene expression microarrays because RBA-Seq A. probes mRNA, while gene expression microarrays probe DNA. B. is able to identify low-abundance, alternatively spliced transcripts. C. does not require the formation of cDNA. D. is based on a pre-determined set of DNA sequences.

Type I topoisomerase activity results in a region of __________ DNA. A) spliced B) none of the above C) unrepaired D) semiconservative E) negatively supercoiled DNA

What is a current hypothesis that explains the infectious nature of prion diseases? A) The small molecule denaturants found in infected cells are passed on to healthy cells B) the presence of an improperly folded prion protein promotes the misfolding of normal prion proteins C) unfavorable environmental factors negatively influence healthy cells D) DNA encodes prion mutant proteins E) the virus responsible for prion diseases is transmissible

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? A) fluorescent labeling B) gel electrophoresis C) polymerase chain reaction D) blue-white screening E) antibiotic resistance

When a protein enzyme folds in an aqueous solution, which of the following is correct? A. Water is always excluded from the active site in the interior of the protein. B. Non-polar amino acids are found in the interior of the protein. C. Polar amino acids are found in the interior of the protein. D. A mixture of polar and non-polar amino acids is found in the interior of the protein.

Which of the following is an intermediate in the conversion of AMP to uric acid but NOT an intermediate in the conversion of GMP to uric acid? A B C D

Which of the following is correct about biological membranes? A. Molecules freely pass through the membrane. B. Biological membranes are made up of a lipid monolayer. C. Phospholipid head groups are directed toward the aqueous environment. D. Phospholipid tails are directed toward the aqueous environment.

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? Choose one or more: A. elevated excretion of HCO3- B. more CO2 exhaled (hyperventilation) C. no change in CO2 exhalation D. diminished HCO3- excretion E. less CO2 exhaled (decreased breathing rate) F. no change in HCO3- excretion

B- more CO2 exhaled (hyperventilation) D- diminished HCO3- excretion

Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf?Choose one: A. CO2 B. osmotic pressure C. air pressure D. dew point

B- osmotic pressure

Which of the following is correct about biological membranes?Choose one: A. Phospholipid tails are directed toward the aqueous environment. B. Phospholipid head groups are directed toward the aqueous environment. C. Biological membranes are made up of a lipid monolayer. D. Molecules freely pass through the membrane.

B- phospholipid head groups are directed toward the aqueous environment

A reaction is always spontaneous if Choose one: A. entropy is increased. B. the change in free energy, ΔG, is negative. C. the change in free energy, ΔG, is positive. D. the change in enthalpy is zero. E. enthalpy is reduced.

B- the change in free energy is negative

Which of the following are properties of water? Choose one or more: A. Water is miscible with oil. B. Water is liquid over a wide range of temperatures. C. Water is polar and an excellent solvent because of its hydrogen-bonding properties. D. Water freezes more readily when ionic solutes are dissolved in it. E. Water is a strong acid at high temperatures. F. Water is less dense as a solid than as a liquid.

B- water is liquid over a wide range of temperatures C- water is polar and an excellent solvent because of its hydrogen-bonding properties F- water is less dense as a solid than as a liquid

30. Which chromophore appears orange and absorbs in the blue range of the visible spectrum?

B-carotene

Which of the following types of chromatin is usually associated with the centromere of a chromosome? Choose one: A. euchromatin B. heterochromatin

B-heterochromatin

What is the concentration of [OH-] in a solution of 0.025 M HCl? Choose one: A. 4.1 × 10-13 M B. 4.0 × 10-13 M C. 1.0 × 10-14 M D. 2.5 × 10-2 M

B. 4.0 × 10-13 M

Which suspect(s) should be further pursued? Base your answer on the DNA evidence alone. Choose one: A. suspect A only B. suspect B only C. both suspects A and B D. neither suspect A nor B

B. suspect B only

In all of the aminotransferases that have been characterized, the catalytic mechanism involves a two-stage reaction in which the α amino group of the amino acid is first transferred to an enzyme-linked pyridoxal phosphate (PLP) group. Pyridoxal phosphate is a coenzyme derivative of vitamin ___

The cross linked nature of the acrylamide media in SDS-PAGE can limit migration through the polymer matrix. Based on the figure to the right put the SDS-PAGE gels in the correct order of lowest to highest acrylamide concentration using A,B, and C

B<C<A

How did the polymerase chain reaction (PCR) revolutionize DNA detection methodologies? Choose the TWO most correct statements below.

Because it is so sequence specific and easy to use, multiple confirmatory data points can be collected, and thereby rule out DNA matches by chance alone. PCR increases the sensitivity of DNA detection in a given sample by up to 1 million fold using a site-specific in vitro DNA synthesis reaction.

Why do inhibitors of Topoisomerase II cause cancer cell death more than neuronal cell death?

Because they inhibit DNA replication; since cancer cells divide frequently, they are preferentially killed

Why do inhibitors of Topoisomerase II cause cancer cell death more than neuronal cell death

Because they inhibit DNA replication;; since cancer cells divide frequently, they are preferentially killed

The effect of pH on O2 binding in the tissues is significant, whereas the effect of pH on O2 binding in the lungs is minimal (very little change in O2 binding as a function of pH in the lungs). Explain this observation Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect. Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the R state as described by the Bohr effect. Because tissues have higher CO2 concentrations than the lungs, which increases the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect. Because tissues have higher O2 concentrations than the lungs, which increases the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect.

Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect.

All of the following are types of protein secondary structure EXCEPT

Beta helixes

sort the following as descriptions of alpha helices, beta sheets, beta turns, or all. -successive R groups point in opposite directions -1st residue hydrogen-bonded to 5th residue (that is, residue n is H-bonded to residue n+4) -all -NH groups point in the same direction -1st residue HB to the 4th residue(residue n is Hbonded to residue n +3) -contains -NH hydrogen bonded to c=o

Beta sheets: -successive R groups point in opposite directions alpha helices: -1st residue hydrogen-bonded to 5th residue (that is, residue n is H-bonded to residue n+4) -all -NH groups point in the same direction beta turns: -1st residue HB to the 4th residue(residue n is Hbonded to residue n +3) all: -contains -NH hydrogen bonded to c=o

Which of the following is a photosynthetic light harvesting pigment? FeS cluster NADPH plastoquinone Beta-carotene

Beta-carotene

Muscle glycogen phosphorylase is regulated by both allosteric effectors, such as AMP and ATP, and by hormonal signaling. Allosteric effectors bind to the phosphorylated and unphosphorylated forms of the enzyme and shift the equilibrium between the inactive T conformation and the active R conformation. In contrast, hormonal regulation involves activation of kinase and phosphatase enzymes, which modulate the phosphorylation status of glycogen phosphorylase. Which TWO statement(s) below best explain the metabolic logic of this dual regulatory mechanism?

Both forms of control are important because they work together to ensure maximum interconversion of glucose and glycogen so that liver cells can maintain safe blood glucose levels at all times. Allosteric regulation by AMP and ATP provides a way to quickly shift the activity of muscle glycogen phosphorylase between the active and inactive states before hormonal signaling is fully stimulated.

Compare the structure of an aldose to a ketose.

Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

Compare the structure of an aldose to a ketose. Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule. Both have a carbon backbone where ketose has a ketone group at the end of the molecule, and aldose also has an aldehyde group at the end of the molecule. Ketose has a carbon backbone with a ketone group at the end of the molecule, whereas aldose has an aldehyde group at the end of the molecule. Ketose has a carbon backbone with an aldehyde group at the end of the molecule, whereas aldose has a ketone group at the end of the molecule.

Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand.

Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution A) had a very high concentration of solvent B) none of these answers are correct C) had no solutes D) had a very high concentration of solutes E) was at equilibrium

The figure below shows part of the primary structure of DNA. Identify the nucleoside.

Which two functional groups are involved in producing a peptide bond? A) none of these answers are correct B) alcohol and amino C) amino and carboxyl D) amino and thiol E) methyl and amino

The titration curve for the amino acid glutamate is shown above. Refer to this figure to answer the following question. The form of glutamate shown above predominates at what point on the titration curve?

C (look this up)

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? A. elevated excretion of HCO3- B. less CO2 exhaled (decreased breathing rate) C. more CO2 exhaled (hyperventilation) D. no change in CO2 exhalation E. diminished HCO3- excretion F. no change in HCO3- excretion

C and E

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? A. no change in CO2 exhalation B. no change in HCO3- excretion C. more CO2 exhaled (hyperventilation) D. less CO2 exhaled (decreased breathing rate) E. elevated excretion of HCO3- F. diminished HCO3- excretion

C and F

Place the following steps in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins C, A, D, B C, B, A, D B, C, A, D C, D, A, B none of these orders are correct.

C, A, D, B

Consider five proteins with the properties shown in the table above and answer the following four questions. Record your answers and choose the set of correct answers for questions a --> d. Note that some proteins may be used more than once and others may not be used at all. a) Which protein would elute last from a gel filtration chromatography column under non-denaturing conditions? b) Which protein would migrate the slowest in an SDS-PAGE gel? c) Which protein would elute last from a (-) charged cation exchange column in buffer at pH 4.0? d) Which protein would elute first from a (+) charged anion exchange column in buffer at pH 4.0?

C, E, A, A

If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water? Choose one: A. The protein would demonstrate no change in water binding. B. The protein would bind water more tightly. C. The protein would not bind water and would lose antifreeze properties. D. The protein would have increased affinity for the phosphate backbone of DNA.

C- The protein would not bind water and would loose antifreeze properties

From the following list, which common substance that you encounter in your daily life has molecular properties similar to the molecules found in biological membranes? Choose one: A. water B. lemon juice C. detergent D. gasoline

C- detergent

Which of the following differentiates the biochemical standard state from the standard state when discussing standard free energy changes?Choose one: A. Constant pressure of 1 atm B. Temperature of 298 K C. pH of 7 D. 1 M concentrations for all reactants and products

C- pH of 7

In the elongation of glycogen, activated glucose units are attached to which hydroxyl of the terminal residue of the growing glycogen chain? C-1 C-3 C-4 C-6

C-4

What distance does proton A appear to travel through the water wire to reach the position marked F? Choose one: A. 10 fm B. 100 pm C. 1 nm D. 1 pm E. 1 µM

C. 1nm

Proton hopping allows for the rapid apparent movement of protons (H+) through aqueous solution. From first to last in the figure above, what is the correct chronological order of proton hopping events (B-E) that form the "water wire" between proton A and proton F? Choose one: A. E → D → C → B B. B → C → D → E C. C → E → B → D D. D → E → B → C

C. C,E,B,D

Which of the following best describes monocistronic and polycistronic genes? Choose one: A. Monocistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while polycistronic genes are encoded in multiple different RNAs. B. Monocistronic genes are only prokaryotic, and polycistronic genes are only eukaryotic. C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein. D. Polycistronic gene products are interpreted by the ribosome, and monocistronic gene products are not.

C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein.

Cancer therapeutics are designed to impact the life of the replicative cell in some way. Some chemotherapy drugs target topoisomerase enzymes. Which of the following statements most accurately describes the effect of these types of anticancer drugs? Choose one: A. These drugs prevent the cell from producing plasma membrane lipids so that the cell cannot grow in size. B. These drugs embed pores in the plasma membrane of cells so that cytoplasm leaks out and the cell apoptoses. C. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest. D. These drugs decrease the ability of the cell to produce ribonucleotides, thereby preventing transcription.

C. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest.

If the same experiment were performed again for the 60 bp DNA, but this time in the presence of 1.5 M NaCl, in what direction would the new curve be positioned compared to the 60 bp DNA that is already in place in this figure? Choose one: A. directly on top of the current curve B. to the left of the current curve C. to the right of the current curve

C. to the right of the current curve

19. The __________ pathway is used by plants that thrive in high temperate conditions, such as sugarcane.

C4 The C4 pathway is found in tropical plants, such as sugarcane, and relies on two different cell types to prevent atmospheric O2 from binding rubisco. The CAM pathway is used by desert succulents, such as cacti, to capture CO2 at night to again prevent atmospheric oxygen from binding rubisco.

27. C4 vs CAM plants

C4: - Malate transferred to bundle sheath cells - Use spatial separation of CO2 fixation and rubisco activity to decrease photorespiration rates - Stomata open during the day. - Sugarcane is an example. CAM: - Malate stored in vacuoles - Use temporal separation of CO2 fixation and rubisco activity to decrease photorespiration rates - Saguaro cactus is an example. - Stomata open only at night

17. What is a major difference between the mechanisms used by C4 and CAM plants to minimize photorespiration and maximize fixation of CO2 by rubisco?

CAM plants allow CO2 to enter the mesophyll cells only at night. The CO2 is stored as malate and then malate is decarboxylated during the day. The CO2 then enters the Calvin cycle. C4 plants capture CO2 in mesophyll cells, convert the CO2 to malate, and transfer the malate to neighboring bundle sheath cells, where the Calvin cycle operates on the CO2 derived from decarboxylated malate.

10. Identify the inputs and outputs of the Calvin cycle.

Calvin Cycle Inputs: CO2, ATP, NADPH Outputs: NADP+, ADP + Pi, Triose phosphates

Which THREE of the following biochemical relationships are correct statements illustrating the hierarchical organization of molecular life?

Carbon, hydrogen, and oxygen are the most abundant elements in biomolecules.Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems.Insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients.

Which separatioin technique exploits the density differences of biomoelcules and organelles?

Centrifugation using centrifuge tubes in a rotor placed in a centrifuge

In the closely packed interior of the tertiary structure of an enzyme, an alanine residue was changed by mutation to a valine, leading to a loss of enzyme activity, although that residue was not directly involved in the catalytic function of the enzyme. However, activity was partially regained when an additional mutation at a different position in the primary structure changed an isoleucine residue to a glycine. Based on the structure of the amino acid side chains of alanine, valine, isoleucine, and glycine, explain how the first mutation Ala→Val likely caused a loss of activity, and the second mutation in another region of the protein, Ile→Gly, resulted in a partial recovery of enzyme activity.

Changing an Ala to a Val would introduce a bulkier side chain, taking up more volume in the protein interior; the resulting structural adjustments in the tertiary structure must be serious enough to cause the enzyme to lose activity. The replacement of an Ile residue with a Gly allows a tertiary structure close enough to the original structure for partial enzyme activity.

Molecular O2 competes with CO2 for the active site of rubisco. When this happens, one of the reaction products is of little metabolic use to the plant. That product is then metabolized by the glycolate pathway, which uses enzymes located in three cellular compartments. Sort the glycolate pathway reactions into their proper cellular compartment.

Chloroplast Oxygenation of RuBP to form 2-phosphoglycolate Transfer of a phosphate group from ATP to glycerate to form 3-phosphoglycerate Peroxisome Conversion of serine to glycerate Transamination of glyoxylate to form glycine Oxidation of glycolate to glyoxylate and release of hydrogen peroxide Mitochondrion Deamination and decarboxylation of glycine to form serine

Which of the following is true concerning cholesterol and plasma membranes? Choose one: A. At high temperatures, cholesterol inhibits membrane fluidity. B. High local concentrations of cholesterol increases membrane fluidity. C. Cholesterol inserts into the membrane via its non-polar planar rings. D. Cholesterol facilitates fatty acid packing.

Cholesterol inserts into the membrane via its non-polar planar rings.

During eukaryotic DNA condensation, nucleosomes are packed together to form genes. histones. genomes. chromatin. chromosomes.

Chromatin

Five coenzymes are needed for the pyruvate dehydrogenase reaction, of which three are covalently linked to proteins int he PDH complex. Name the two coenzymes that are diffusible within the matrix.

CoA and NAD+

How would someone that has a G6P dehydrogenase deficiency attempt to mitigate the symptoms of the genetic disease?

Consume more five carbon-containing foods.

For the cAMP-mediated pathway, identify the following components: Second messenger produced by Second messenger Kinase Result 1. cAMP 2. Adenylate cyclase 3. Protein kinase A (PKA) 4. Glucose mobilization 5. diacylglycerol (DAG) 6. phospholipase C (PLC) 7. protein kinase C (PKC) 8. Glucose storage (as glycogen)

Correct Response __2__ Second messenger produced by Correct Response __1__ Second messenger Correct Response __3__ Kinase Correct Response __4__ Result

The importance of stable free radicals in the mechanism of E. coli ribonucleotide reductase was identified in the early 1970s. The existence of stable radicals in a protein had not been previously observed. Which of the following amino acids can exist as a stable radical in ribonucleotide reductase? Cys His Ser Glu

Cys

15. Which of the following is responsible for transporting protons across the thylakoid membrane?

Cytochrome b6f

Which of the following enzymes is NOT necessary for producing the monounsaturated oleoyl-CoA? Choose one: A. Stearoyl-CoA 9-desaturase B. Cytochrome b5 reductase C. Cytochrome b5 D. Cytochrome c

Cytochrome c

A polypeptide has a high pI value. Which amino acids might comprise it? A) a mixture of aspartate and arginine residues B) aspartate and glutamate residues C) none of the above D) arginine and lysine residues E) the large nonpolar amino acids

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located? mc031-1.jpg

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located? A C D B

Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA?

Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA? C A B none of these answers are correct. D

Energy conversion in living systems is required for what three types of work? A) none of the above B) osmotic work, photosynthetic work, mechanical work C) kinetic work, chemical work, mechanical work D) osmotic work, chemical work, mechanical work E) osmotic work, chemical work, potential work

Fatty acids are amphipathic, meaning that within the molecular structure, A. both ends repel from water; they are both hydrophobic. B. both ends interact with water; they are both hydrophilic. C. one end is negatively charged and the other end is positively charged. D. one end is polar and the other end is nonpolar.

How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment? A) semipermeable cell walls B) photosynthesis C) flexible cells walls D) none of these answers are correct E) they lack cell walls

How many possible unique triplet codons could there be in a genome? A) 72 B) 3 C) 36 D) none of the above E) 20

Limonene is a nonpolar molecule. The water molecules around it forms A) none of the above B) covalent bonds with limonene and entropy increases C) ionic bonds with itself and the entropy decreases D) hydrogen bonds with itself and entropy decreases E) hydrogen bonds with limonene and the entropy increases

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first? Peptide Molecular Weight (g/mol) Charge A 360 -2 B 1080 -1 C 1800 0 D 1440 +1

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first? Peptide, Molecular Weight (g/mol), Charge A, 360, -2 B, 1080, -1 C, 1800, 0 D, 1440, +1

What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group, and 10.5 for the side chain amino group? A. 6.3 B. 5.9 C. 7.0 D. 10.1

What mediates the binding of histone proteins to DNA? A) hydrophilic interactions B) hydrophobic interactions C) London dispersion forces D) ionic attractions E) none of the above

When a protein enzyme folds in an aqueous solution, which of the following is correct? A. Water is always excluded from the active site in the interior of the protein. B. A mixture of polar and non-polar amino acids is found in the interior of the protein. C. Polar amino acids are found in the interior of the protein. D. Non-polar amino acids are found in the interior of the protein.

Which of the following is correct about biological membranes? A. Phospholipid tails are directed toward the aqueous environment. B. Molecules freely pass through the membrane. C. Biological membranes are made up of a lipid monolayer. D. Phospholipid head groups are directed toward the aqueous environment.

Which of the following pairs contain terms that would be considered synonyms of one another regarding DNA integrity? A. annealed : melted B. denatured : annealed C. denatured : renatured D. melted : denatured E. renatured : annealed

D and E

The genetic anomaly that leads to HGPS is a cytosine Choose one: A. amination. B. carboxylation. C. decarboxylation. D. deamination.

D- deamination

Placed in a hypertonic solution, a living cell will Choose one: A. absorb water and get larger. B. remain unchanged. C. decrease the pH of the cytoplasm to stop water movement. D. shrink as water leaves the cell.

D- shrink as water leaves the cell

Which of the following steps is performed when preparing to do both an RNA-seq analysis and a gene microarray? Choose one: A. Generate fluorescently labeled RNA fragments. B. Convert RNA to complementary DNA called cDNA. C. Create high-throughput DNA sequencing. D. Isolate mRNA from whole cell lysate.

D. Isolate mRNA from whole cell lysate.

On this graph, the curves shift to the right as the G-C content increases. This is because G and C are connected by Choose one: A. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. B. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher. C. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.

D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.

Which of the following biochemical reactions are endergonic?Choose one or more: A.ATP ⇒ ADP + Pi ; Δ𝐺∘ΔG∘ = −30.5 kJ/mol B.Acetyl-CoA + Oxaloacetate + H2O ⇒ Citrate + CoASH + H+ ; Δ𝐺∘ΔG∘ = -32.2 kJ/mol C.Glutamate + NH4+ + ATP ⇒ Glutamine + ADP + Pi ; Δ𝐺∘ΔG∘ = −16.3 kJ/mol D.L-Malate + NAD+ ⇒ Oxaloacetate + NADH + H+ ; Δ𝐺∘ΔG∘ = +29.7 kJ/mol E.Glutamate + NH4+ ⇒ Glutamine; Δ𝐺∘ΔG∘ = +14.2 kJ/mol

D.L-Malate + NAD+ ⇒ Oxaloacetate + NADH + H+ ; Δ𝐺∘ΔG∘ = +29.7 kJ/mol E.Glutamate + NH4+ ⇒ Glutamine; Δ𝐺∘ΔG∘ = +14.2 kJ/mol

Succinate dehydrogenase is the citrate cycle enzyme that catalyzes the conversion of succinate into fumarate, and in the process converts FAD to FADH2. Use the standard reduction potentials given below for the reduction reactions to calculate the standard free energy change for the reaction. (Note that the value for FAD given here estimates the reduction potential for FAD when bound to succinate dehydrogenase.) FAD + 2H+ + 2e- ---> FADH2 Eo' = 0.035 V Fumarate + 2H+ + 2e- ---> Succinate Eo' = 0.031 V DGo' = -0.77 kJ/mol DGo' = 12.7 kJ/mol DGo' = 0.77 kJ/mol DGo' = 0.38 kJ/mol DGo' = -12.7 kJ/mol DGo' = -0.38 kJ/mol

DGo' = -0.77 kJ/mol

gene segments of ___ are functional units defined by nucleic acid products they produce

DNA

Match the polymer with the monomer that can be one of its components. DNA Glycogen phosphorylase Glycogen 1. Glucose 2. ATP 3. Glutamate

DNA - 2. ATP Glycogen phosphorylase - 3. Glutamate Glycogen - 1. Glucose

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?

DNA ligase

Which of the following is not a transport protein?

DNA polymerase

What do o factors bind to in RNA synthesis? DNA promoters and RNA polymerase RNA promoters and DNA DNA and RNA transcription factors

DNA promoters and RNA polymerase

You are preparing for a debate about climate change. Which of the following statements would support the idea that preservation of forests, or even expanding the world's forests, would help stabilize the greenhouse effect?

Decreasing global production of CO2 by burning fewer fossil fuels, for example, would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms. Expanding the amount of the Earth covered by forests and other photosynthesizing organisms would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms.

If the equilibrium constant (Keq) is greater than 1, what is the value of delta Gº? Delta Gº=1 Delta Gº>0 Delta Gº>1 Delta Gº<0

Delta Gº<0

If a reaction has a DeltaH > 0 and a DeltaS < 0, then __________ and the reaction is __________ at all temperatures.

DeltaG > 0 and nonspontaneous

If the equilibrium constant (Keq) is greater than 1, what is the value of DeltaG o? DeltaG o>1 DeltaG o>0 DeltaG o=0 DeltaG o<0

DeltaG o<0

When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase, the final mixture contains twice as much glucose 6-phosphate as fructose 6-phosphate. Which one of the following statements is MOST correct, when applied to the reaction below (R = 8.315 J/mol·K and T = 298 K)? Glucose 6-phosphate ↔ fructose 6-phosphate

DeltaG'o is +1.7 kJ/mol

DeltaG`º is +1.7 kJ/mol.

As DNA unwinds and denatures, absorbance is predicted to A) reamain the same B) decrease C) none of the above D) vary unpredictably E) increase

The fluidity of a membrane depends on A) osmotic pressure B) the size of the polar head group C) the number of phospholipids in the membrane D) the protein composition E) the degree of saturation of the phospholipids

The sequencing of the human genome has been instrumental toward A. the field of individualized/personalized drug development. B. our understanding of the genetic basis of disease. C. better genetic counseling to prospective parents. D. a more complete understanding of Homo sapiens' molecular inheritance. E. All of these areas were enhanced by the sequencing of the human genome.

Type II topoisomerase enzymes are important in replication and transcription because they A) prevent DNA cleavage B) stabilize the cleaved complex C) none of the above D) prevent autocleavage E) relieve the positive supercoiling

Which of the following are negatively charged amino acids at pH = 7? A) Cys, Asn B) Thr, Tyr C) Gln, Asn D) none of the above E) Glu, Asp

Which of the following statements regarding protein domains is true? A) a domain is a region absent of alpha helices and beta sheets B) each protein has one unique domain C) multiple domains require multiple subunits and quaternary structure D) a motif can be composed of smaller structural units called domains E) none of the above

Which stabilizing force in protein tertiary structures is a covalent bonding force? A) van der Waals B) ionic C) none of the above D) hydrophobic E) disulfide bonding

To purify glutathione reductase to carry out a kinetics analysis, which organism would be the best source of the enzyme? cod fish chimpanzee E. coli turtle

E. coli

Calculate the energy charge of the cell assuming that the concentration of ATP, ADP, and AMP were all equal. Why is this value not a good representation of actual energy charge in a healthy cell? EC = 0.5; because ATP levels are normally higher and AMP levels are normally lower. EC = 0.5; because ATP levels are normally lower and AMP levels are normally higher. EC = 0.7; because ATP levels are normally lower and AMP levels are normally lower. EC = 1.0; because ATP levels are normally higher and AMP levels are normally lower. EC = 0.9; because ATP levels are normally lower and AMP levels are normally higher.

EC = 0.5; because ATP levels are normally higher and AMP levels are normally lower.

After the initiation complex is complete, what occurs next in the process of translation? peptide bond formation EF-G•GTP binding EF-Tu•GTP^AA-tRNAAA binding RF2 binding

EF-Tu•GTP^AA-tRNAAA binding

Which of the following statements best supports the idea that photon absorption by chlorophyll is an all-or-none phenomenon?

Each delocalized electron above and below the porphyrin ring possesses an energy difference with its adjacent orbital that corresponds to the energy of a photon within the visible light range.

Choose the one TRUE statement from the choices below regarding peptide synthesis

Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide.

Choose the one TRUE statement from the choices below regarding peptide synthesis None of these answers are correct. Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide. Peptide synthesis in the lab cannot incorporate proline residues due to the ring structure of this amino acid. Peptide synthesis in the lab can only be done for short peptides due to the high cost of the reagents involved. Peptide synthesis in the lab requires that the side chain are deprotected prior to their addition to the growing peptide chain.

Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide.

8. Which of the following statements is correct about the flow of electrons in photosystem I?

Electrons enter PSI from electron carriers in the thylakoid lumen and exit PSI via electron carriers in the stroma. All electron carriers in PSI are embedded in the thylakoid membrane.

Within a eukaryotic cell, is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis:

Endoplasmic Reticulum

Within a eukaryotic cell, the _________ is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis.

Endoplasmic reticulum

Liver cells were monitored for changes in metabolic enzymatic activity after exposure to glucagon. The enzymes that showed changes in activity were then analyzed to assess if they had been covalently modified. Which of the following results were likely observed? None of these answers are correct. Enzymes that showed altered activity (higher or lower) were phosphorylated. Enzymes that showed lower activity were not phosphorylated. Enzymes that showed higher activity were methylated. Enzymes that showed altered activity (higher or lower) were methylated.

Enzymes that showed altered activity (higher or lower) were phosphorylated.

according to the hierarchal levels organize the following: a. bird b. cytoplasm c. glycolysis d. simple sugar e. carbs f. oxygen g. forest

F,D,E,C,B,A,G

Which of the following is a coenzyme that is derived from ATP? coenzyme Q FAD heme Fe4-S4 cluster

FAD

Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?

FADD

What is the "cost" of using the glycerol-3-phosphate shuttle instead of the malate-aspartate shuttle in terms of proton-motive force and ATP synthesis? (choose one correct answer). For the glycerol-3-phosphate shuttle, electrons are transferred to NAD to form NADH, resulting in 4 more translocated H+, and more ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to NAD to form NADH, resulting in 4 fewer translocated H+, and less ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to form FADH2, resulting in 4 more translocated H+, and more ATP synthesis.

For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis

Two amphipathic α helices in a dilute aqueous solution are likely to: None of these answers are correct. rearrange into β sheets in order to stack against each other to bury hydrophobic side chains. repel each other and remain as individual helical molecules. form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle. form a coiled coil structure with the polar amino acid side chains interacting with each other down the middle.

Form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle.

Which FOUR statements are true regarding β sheets?

Found in globular proteins Stabilized by H-bonds between -NH and -CO groups An extended conformation of the polypeptide chain The stability is affected by amino acid sequence

The same four reactions that are central to the beta-oxidation pathway are also present in the fatty acid synthesis pathway, except they are reversed. What is a key difference between the four reactions in these two pathways? One set of reactions synthesizes an ATP, whereas the other set uses an ATP. One set occurs in the muscle, whereas the second pathway occurs in the liver. One pathway adds three carbon atoms at a time, whereas the other removes two carbons. Four enzymes are used in one, whereas one enzyme is used in the other.

Four enzymes are used in one, whereas one enzyme is used in the other.

In comparison with glycerophospholipids and sphingolipids, cholesterol contains: A. Four steroid rings B. Glycerol moiety C. Phosphate group D. Three steroid rings E. Choline head group

Four steroid rings

25. Which of the following are common features of glycoconjugates?

Frequently contain the hexosamine N-acetylgalactosamine Are covalently attached to lipids and proteins Contain both modified and unmodified monosaccharides

12. Where does the CO2 come from that is used in the Calvin cycle?

From the air

In the second temperature phase of PCR, why does the temperature vary from 55 d Celsius to 65 d Celsius?

G-C content

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer).

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer). More DNA binding proteins bind to G-C rich regions, and therefore stabilize these structures. None of these answers are correct. Counterions (like Mg2+) bind preferentially to G-C rich regions, enhancing their stability. G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions The primary reason G-C rich regions are more stable is that G-C base pairs have three hydrogen bonds, and A-T base pairs have only two hydrogen bonds.

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer). The primary reason G-C rich regions are more stable is that G-C base pairs have three hydrogen bonds, and A-T base pairs have only two hydrogen bonds. Counterions (like Mg2+) bind preferentially to G-C rich regions, enhancing their stability. More DNA binding proteins bind to G-C rich regions, and therefore stabilize these structures. G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

How are changes in enthalpy (H) and entropy (S), related to changes in free energy (G)? Given the following common reactions, which are entropically favored?

G=H-T delta S ATP ⇒ ADP + Pi

An inhibitor of __________ would specifically prohibit the release of Ran from importin. GTP-GDP exchange in Ran exportin the signal peptide peptidase GAP

GAP

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA GLMKTY PDSTA GLMK TYPDSTA GLM KTYPDSTA GLMKTYPD STA

GLMK TYPDSTA

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA GLMKTY PDSTA GLMKTYPD STA GLMK TYPDSTA GLM KTYPDSTA

GLMK TYPDSTA

creutzfeld and jakob disease

GOF

huntington's disease is caused by a

GOF mutation

After inhalation of the asthma drug fluticasone, what two signaling mechanisms mediated by the glucocorticoid receptor lead to a decrease in airway inflammation and relief of asthma symptoms?

GR blocks NFkB induction of Cox2 gene expression and GR activates expression of the annexin gene

Which amino acid side chain from the list below is the most polar? Leu Gln Ala Phe

Gln

Which of the following are negatively charged amino acids at pH = 7?

Glu, Asp

Based on the structures of D-glucose and D-galactose (shown below), which of the following statements is true?

Glucose and galactose are epimers of each other.

Based on the structures of D-glucose and D-galactose (shown below), which of the following statements is true? Glucose and galactose are tetroses. Glucose and galactose are epimers of each other. Glucose and galactose are ketoses. none of these statements are correct. Glucose and galactose are anomers of each other.

Glucose and galactose are epimers of each other.

Which of the following occurs after activation of the PI-3K signaling pathway?

Glucose uptake increases.

Which of the following occurs after activation of the PI-3K signaling pathway? Glycogen synthesis rates decrease. PTEN protein dimerizes. GLUT-1 levels decrease. Glucose uptake increases. GRB2 is activated.

Glucose uptake increases.

Which of the reactions below is the balance reaction for the catabolism of glucose to lactate?

Glucose+2ADP+2Pi->2ATP+2H2O

For the yeast biochemical pathway, identify fermentative reactants and products by dragging the chemical names to their respective structures Within the biochemical pathway in Part 1, which chemical contains completely oxidized carbon atoms?

Glucose, Ethanol, Carbon dioxide Carbon dioxide

If protein kinase A is activated in a liver cell in response to glucagon binding to the beta2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on.

Which of the following is a reactant in the net reaction of the citrate cycle?

H2O

Nonprimate mammals convert uric acid to allantoin. This reaction, catalyzed by urate oxidase, also generates which of the following products? H2O H2O2 O2 NH4+

H2O2

What molecules are missing from boxes in the gluconeogenesis reaction shown below? Ser-Pi; Ser-Pi H2O; Pi ADP; ATP ATP; ADP

H2O; Pi

given a solution with pH > pKa, what are the relative concentrations of H and HA

HA < A

Weak acids have a high pka because

HA concentration is high

In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support?

An enzyme panel analysis of a patient reveals a lack of __________, which is an indication of Lesch-Nyhan syndrome. PRPP synthetase adenosine deaminase HGPRT xanthine oxidase

HGPRT

If a Glu sidechain is in a hydrophobic environment, would you expect that the pKa of this sidechain would be higher or lower than the pKa for the sidechain in aqueous solution? (choose one correct answer).

HIGHER

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin? His57 Ser195 Asp102 Gly193

HIs57

Glycan arrays can be coupled with __________ to qualitatively compare fractionated cell extracts from different sources. MALDI-TOF HPLC size exclusion chromatography mass spectrometry

HPLC

Which statement most accurately describes the structure and function of O2 transport proteins

Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG

Which statement most accurately describes the structure and function of O2 transport proteins? Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG. Leghemoglobin, myoglobin, and hemoglobin all have one thing in common; they bind CO2 very tightly. Myoglobin is found in skeletal muscle, red blood cells, and adipose tissue; hemoglobin is in heart muscle. None of the above statements is correct. Hemoglobin and myoglobin are identical in structure with the only difference being the color of the heme.

Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are true?

Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration.The majority of autotrophs on Earth require aerobic respiration in order to survive.Heterotrophs depend on autotrophs for conversion of light energy to chemical energy.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE?

Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. The majority of autotrophs on Earth require aerobic respiration in order to survive.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE? Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. Autotrophs depend on heterotrophs to oxidize sugar and release CO2 into the atmosphere. Heterotrophs evolved on Earth before autotrophs. There are no metabolic differences between autotrophs and heterotrophs. Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. Heterotrophs that do not eat autotrophs every day will die in a short time. The majority of autotrophs on Earth require aerobic respiration in order to survive. The majority of heterotrophs on Earth do not use aerobic respiration as a form of energy conversion.

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell.

High AMP concentrations,Low ATP concentrations,The energy charge ratio is below 0.70

Which of the following is true regarding the roles of adenylylation and uridylylation in the control of glutamine synthetase?

High levels of ATP and α-ketoglutarate result in more deadenylylated glutamine synthetase.

Higher

Which of the following pairs of amino acids need glutamine to be generated, but are also both allosteric regulators of glutamine synthetase? Choose one: A. Alanine, serine B. Serine, tryptophan C. Glycine, histidine D. Histidine, tryptophan

Histidine, tryptophan

A scientist can use a variety of bioinformatic tools to compare the DNA of individuals suffering from a genetic disease to the DNA of unaffected individuals. Why, then, do scientists try to identify the gene involved in the disease before searching for a specific mutation?

Human genomes contain many random mutations that have little to no effect on protein expression or function. Some are spontaneous, whereas SNPs and STRs are inherited. Simply comparing the DNA of two individuals would result in the identification of hundreds to thousands of differences. If the affected gene is known, then the sequence of that gene from an affected individual can be compared to unaffected individuals, including parents or siblings, in order to help eliminate inherited variations as potential disease-causing mutations.

Why does hydrogen bonding between base pairs contribute little to overall helix stability?

Hydrogen bonding occurs between bases within a DNA double helix, but when DNA strands are denatured, the hydrogen bonds are replaced by hydrogen bonds between bases and water that are similar in strength.

Hydrolysis of ATP is an exergonic reaction

Match the 4 amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A). Chemical groups: hydrophobic, hydrophilic, aromatic, charged Amino acids: Serine, Phenylalanine, Aspartate, Isoleucine

Hydrophobic - Isoleucine Hydrophilic - Serine Aromatic - Phenylalanine Charged - Aspartate

Match the four amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A).

Hydrophobic-Valine Charged- Arginine Hydrophilic- Threonine Aromatic- Tryptophan

Enzyme deficiencies that affect the fatty acid β-oxidation pathway are often diagnosed by examining the different metabolic intermediates in the bloodstream. An individual with a deficiency in an enzyme required for β oxidation would have which of the following results if the ketone bodies and glucose concentration of their blood were tested after fasting? Choose one: A. Ketotic hypoglycemia B. Hypoketotic hypoglycemia C. Hyperketotic hypoglycemia D. Ketotic hyperglycemia

Hypoketotic hypoglycemia

lambert-beers law with intensity

I0= intensity of incident light I = intensity of transmitted light

Use the table below to answer the question. In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc018-5.jpg O2 + NADH II. FADH2 + H2O mc018-6.jpg O2 + FAD III. NADH + O2 mc018-7.jpg H2O + NAD+ I and III I, II, and III II only II and III III only I and II I only

III only

Use the table below to answer the question. Standard Reduction Potentials (mc018-1.jpg) for Half Reactions NAD+ + H+ + 2 e− mc018-2.jpg NADH −0.32 V FAD + 2 H+ + 2 e− mc018-3.jpg FADH2 −0.22 V O2 + 4 H+ + 4 e− mc018-4.jpg 2 H2O +0.82 V In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc018-5.jpg O2 + NADH II. FADH2 + H2O mc018-6.jpg O2 + FAD III. NADH + O2 mc018-7.jpg H2O + NAD+

III only

Use the table below to answer the question. In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc227-5.jpg O2 + NADH II. FADH2 + H2O mc227-6.jpg O2 + FAD III. NADH + O2 mc227-7.jpg H2O + NAD+

III only

Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes?

IKK

Select the TWO true statements below describing the standard free energy change (delta G) and the equilibrium constant (Keq). The equilibrium constant is equal to ratio of the concentration of reactants over products at equilibrium. If the value of the equilibrium constant is known, the value for the standard free energy change can be determined. The value for the standard free energy change is constant for a given reaction. The standard free energy change is a function of enzyme concentration in the reaction. A reaction is spontaneous when the standard free energy change and the equilibrium constant are both negative values.

If the value of the equilibrium constant is known, the value for the standard free energy change can be determined. The value for the standard free energy change is constant for a given reaction.

Beriberi is a nutritional deficiency disorder that causes debilitating neurological symptoms. Why do individuals with beriberi have a large amount of pyruvate in their blood following a high-carbohydrate meal? (choose one correct answer). Individuals with beriberi cannot readily metabolize pyruvate to phosphoenolpyruvate because succinyl-CoA synthase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to phosphoenolpyruvate because pyruvate dehydrogenase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because pyruvate dehydrogenase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because succinyl-CoA synthase is inactive without thiamine pyrophosphate.

Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because pyruvate dehydrogenase is inactive without thiamine pyrophosphate

beers law image

Io light bulb >>> monochrometer>>> Sample>>>> I(intensity of transmitted light) ^c=conc. length of sample=l

How do we deal with the double bonds during the degradation of unsaturated fatty acids? Convert the three-carbon propionyl-CoA to succinyl-CoA and feed it into the TCA cycle. Converge them with the TCA cycle to produce acetyl-CoAs. Isomerize the position of the double bonds to converge them with the beta-oxidation pathway. Reduce them to single bonds and feed the saturated fatty acid into the beta-oxidation pathway.

Isomerize the position of the double bonds to converge them with the beta-oxidation pathway.

To study red blood cells without damaging them through osmotic shock, they should be kept in a solution which is... (choose one correct answer).

Isoonic

To study red blood cells without damaging them through osmotic shock, they should be kept in a solution which is... (choose one correct answer). Hypertonic Hypotonic Allosteric Isotonic At the pI

Isotonic

Which of the following is true of the glyoxylate cycle? It allows plants to produce glucose from fats and two-carbon molecules like acetate. It occurs in plant cells as an alternative to photosynthesis. It bypasses all regulated steps of the TCA cycle. It results in a net production of ATP and NADH without proceeding through the TCA cycle.

It allows plants to produce glucose from fats and two-carbon molecules like acetate.

Which of the following is true of procaspase 8?

It can be activated by proteolysis.

Which of the following is true of procaspase 8? It is a kinase. It is proteolytically active. It can cleave caspase 3. It can be activated by proteolysis.

It can be activated by proteolysis.

18. What is a oligosaccharide?

It contains more than two monosaccharide residues connected by a glycodisic bond. Oligosaccharides generally contain between three and twenty residues.

16. Having PSII and PSI complexes unevenly distributed in the thylakoid membrane offers several advantages for the light reactions of photosynthesis. Among the reasons below, which is not correct?

It ensures that plastocyanin and ferredoxin, soluble electron carriers associated with PSII and PSI, respectively, are able to come into close contact and transfer electrons with each other during cyclic photophosphorylation. Plastocyanin is in the thylakoid lumen, and ferredoxin is in the stroma. The thylakoid membrane prevents them from contacting each other.

Which of the following is true of the induced-fit model of enzyme catalysis but NOT of the lock and key model of enzyme catalysis?

It involves a conformational change of the enzyme

Which of the following is NOT a reason why glycolysis is considered one of the core metabolic pathways in nature?

It is a primary pathway for nitrogen generation.

Which of the following is correct concerning methicillin?

It is produced by synthetic antibiotic.

Which of the following is true of sickle cell anemia?

It results in a hemoglobin that contains a hydrophobic amino acid on its surface

Suppose the alpha amino group of a protein has a pKa of about 8 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8 if the alpha amino group were buried in the hydrophobic interior of the protein and why?

It would be lower because the alpha amino group would be uncharged at neutral pH, which is favorable.

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha-amino group of a protein has a pKa of about 8.0 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8.0 if the alpha-amino group were buried in the hydrophobic interior of the protein and why? It would be the same because the hydrophobic environment would have no effect on the pKa. It would be lower because the hydrophobic environment has more water and less hydroxyl groups. It would be higher because the hydrophobic environment would provide stability to the proton. It would be higher because the alpha-amino group would be uncharged at neutral pH, which is favorable. It would be lower because the alpha-amino group would be uncharged at neutral pH, which is favorable.

It would be lower because the alpha-amino group would be uncharged at neutral pH, which is favorable.

For the reaction: A + B ↔ C + D, which of the following is correct?

Keq = [C][D]/[A][B]

For the reaction: A + B ↔ C + D, which of the following is correct? Keq = [A][B]/[C][D] ΔG° = RT ln Keq Keq = [C][D]/[A][B] ΔG° = -RT log Keq

Keq = [C][D]/[A][B]

for the reaction A+B<-> C+D which of the following is correct

Keq= [C][D]/[A][B]

Which lipid is thought to give rise to the plaques that can clog arteries? HDL LDL VLDL chylomicrons

LDL

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

LMYKWDERMGFCE

cystic fibrosis mutation

LOF

The human gut microbiome is a collection of microbes that are necessary for proper function of the digestive system and that contribute to the overall health of the individual. Infants are colonized with these microbes at birth and their nutrition in the early days of life is important for supporting growth of these microbes. Milk sugars are important in development of the microbiome. Which of the following best explains how both lacto-N-tetraose and lacto-N-fucopentaose could contribute to proper development of an infant's microbiome?

Lacto-N-fucopentaose binds to surface receptors on pathogenic bacteria and prevents them from entering epithelial cells in the intestine. Lacto-N-tetraose is a food source for bacteria that aid in digestion of this and other oligosaccharides.

29. Which of the following is an example of a disaccharide?

Lactose

The Biosphere 2 project, in Tucson, Arizona, was an experiment involving a large sealed terrarium with humans and photosynthetic plants living in balance. Why did the project have to be interrupted after only a few months? Levels of CO2 rose to dangerous levels. The humans ran out of food. The plants stopped producing oxygen. The rate of photosynthesis was too high.

Levels of CO2 rose to dangerous levels.

Choose the four TRUE statements below regarding receptor tyrosine kinases. Ligand binding is required for autophosphorylation (cross-phosphorylation) The structure includes a transmembrane helix The alpha subunit contains seven alpha helices that span the membrane RTKs are dimeric in the presence of ligand The ligand binds to the extracellular domain The intracellular domian has phosphatase domains

Ligand binding is required for autophosphorylation (cross-phosphorylation) The structure includes a transmembrane helix RTKs are dimeric in the presence of ligand The ligand binds to the extracellular domain

In addition to a ligand binding site, PPARgamma/RXRalpha complexes also contain coregulator binding sites that bind LXXLL peptides. Select the one TRUE statement below.

Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins.

In addition to a ligand binding site, PPARgamma/RXRalpha complexes also contain coregulator binding sites that bind LXXLL peptides. Select the one TRUE statement below. The coregulator binding site selects for phosphorylated LXXLL peptides, so that ligand binding can be modulated by phosphorylation. Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins. The coregulator binding site is located on the face of PPAR/RXR that binds DNA, to prevent DNA binding when the coregulator is bound. Only RXRalpha binds the coregulator, which enhances ligand binding by PPARgamma.

Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins.

In the opening sequence of the video, a protein is "unraveled" down to an extended linear conformation. Which of the following statements accurately captures what is happening in this process?

Linearizing the polypeptide destroys the spatial relationships that define secondary and tertiary structure.

Of these three parameters regarding DNA twist, which is calculated by adding the other two parameters together

Linking number (Lk)

How does glycogen metabolism differ between muscle and liver cells? A. Glycogen degradation is stimulated by glucagon in liver cells but insulin in muscle cells. B. Glycogen particles in muscle cells has fewer a-1,6-glycosidic bonds than glycogen in liver cells. C. Liver cells contain glucose-6-phosphatase, which dephosphorylates glucose-6P to release glucose. D. The glycogen phosphorylase enzyme in liver cells is activated acetyl-CoA rather than ATP. E. Glycogen metabolism in muscle cells produces palmitate from acetyl-CoA, but myristate in liver cells

Liver cells contain glucose-6-phosphatase, which dephosphorylates glucose-6P to release glucose.

Which of the following sequences is most likely a nuclear localization signal? Lys-Lys-Arg-Gly-Arg Glu-Asp-Asp-Gly-Glu Ile-Leu-Phe-Leu-Gly Lys-Asp-Arg-Glu-Glu

Lys-Lys-Arg-Gly-Arg

A mutation in the beta subunit of hemoglobin is discovered that reduces the affinity of 2,3-BPG binding. Which of the following mutations is most likely to have this consequence?

Lys82 -> Asp82

31. Which of the following is an example of a monosaccharide?

Mannose

Which of the statements below best describes the mechanism of proton translocation via a redox-driven conformational change?

Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane.

Which of the statements below best describes the mechanism of proton translocation via a redox-driven conformational change? When the e- binds to cytochrome c, it results in dissociation of cytochrome c from complex III, which stimulates release of H+ from complex III. Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane. A redox reaction results in a H+ and e- that are separated within the transmembrane electron transport system and deposited on opposite sides of the inner mitochondrial membrane. The e- is used to reduce an oxidant, and the H+ is released into the intermembrane space. The flow of coenzyme Q between complex I and complex III alters membrane fluidity, which makes the membrane briefly permeable to protons.

Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane.

- Flippases are enzymes that catalyze the flip-flop movement of phospholipids in a membrane bilayer. What property of membranes contributes to the energy barrier that flippases lower in order to increase the rate of phospholipid flipping?

Membranes consist of a phospholipid bilayer, which means that it has a polar surface on both sides and a hydrophobic center layer. For a phospholipid to flip, the polar head group has to pass through the hydrophobic layer and that is an energy barrier that is lowered by the flippase enzyme, most likely by shielding the head group

C4 plants inhibit photorespiration and increase CO2 fixation efficiency by separating the capture of CO2 and the Calvin cycle into two adjacent cell types. Sort the following reactions based on whether they occur in mesophyll cells or bundle sheath cells.

Mesophyll Cells: Reduction of oxaloacetate to malate Pyruvate + ATP → PEP HCO3- + PEP → oxaloacetate Bundle Sheath Cells: Malate + NADP+ → Pyruvate + NADPH + CO2 Calvin cycle Glyceraldehyde-3-P → Starch and Sucrose

Which of the following common functional groups in biomolecules is NOT capable of multiple protonation states?

Methyl

Using the table below, determine the kind of gene mutation illustrated. ATG_AAT_CAC -> ATG_AAG_CAC frameshift mutation silent mutation nonsense mutation missense mutation

Missense mutation

In on type of hemoglobin mutant the amino acid change generates a strong ionic interaction stabilizing the T state conformation but only under conditions of lower pH, e.g., at pH 7.2 compared to pH 7.6. What effect would this mutation have on the amount of O2 delivered to the tissue and why

More O2 delivered to the tissue because the RT equilibrium would be shifted to the T state in tissues

Why is it important that muscle cells are unresponsive to glucagon? Muscle cells store glycogen for its own energy needs and not the needs of other tissues. The muscles do not store glycogen. The muscles release glucose to other tissues in need. Muscle cells respond to insulin instead.

Muscle cells store glycogen for its own energy needs and not the needs of other tissues.

given the partial sequence of a peptide: ILWANRMSHVLFAVEA which amino acid residues would you expect to be on the solvent-exposed surface once it folds into its native conformation

N,R,S,H,E

The DNA alkylation of guanine is possible because the __________ of guanine is __________ and reacts rapidly with __________ alkylating agents. N-7; nucleophilic; electrophilic N-5; nucleophilic; electrophilic N-7; electrophilic; nucleophilic N-5; electrophilic; nucleophilic

N-7; nucleophilic; electrophilic

What is the fate of NADH after it donates its electrons to the electron transport system?

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

What is the fate of NADH after it donates its electrons to the electron transport system? NAD+ is fed into the TCA cycle for oxidation of CO2. none of these answers are correct. NAD+ is excreted from the cell and sent to the liver for final degradation. NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated. NADH is used for cellular biosynthesis.

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

Which molecule in the net reaction of the citrate cycle contributes to the inhibition of pyruvate dehydrogenase?

NADH

Which reaction does the concept of oxidative phosphorylation refer to?

NADH + 1/2 O2 + H+ + ADP + Pi --> NAD+ + ATP + H2O

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?

NCCNCC

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace? NCCNCC CNCCNC NCONCO NCCONCCO

NCCNCC

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace? NCCNCC CNCCNC None of these answers are correct. NCONCO NCCONCCO

NCCNCC

Which of the following is the net reaction of the urea cycle? Urea + Fumerate + 2 ADP + 2Pi + AMP + PPi --> NH+ + HCO3- + aspartate + 3ATP NH+ + HCO3mc123-2.jpg + aspartate + 3ATP --> urea + fumerate + 2 ADP + 2Pi + AMP + PPi NH+ + HCO3mc123-4.jpg + fumerate + 3ATP --> urea + aspartate + 2 ADP + 2Pi + AMP + PPi NH+ + HCO3mc123-6.jpg + aspartate + 2 ADP + 2Pi + AMP + PPi --> urea + fumerate + 3ATP

NH+ + HCO3mc123-2.jpg + aspartate + 3ATP --> urea + fumerate + 2 ADP + 2Pi + AMP + PPi

helices notation

Nm N=number of turns m=number of atoms

28. Which of the following is FALSE concerning cyclic photophosphorylation?

No NADP+ is produced

Does hydrogen bonding between base pairs account for the overall stability of the DNA helix

No, because hydrogen bonding between bases in the DNA helix is replaced by hydrogen bonding with water in single strand DNA, therefore hydrogen bonding is in sufficient to explain why DNA helix is stable

Does hydrogen bonding between base pairs account for the overall stability of the DNA helix?

Two-dimensional polyacrylamide gel electrophoresis separates proteins based on shape and ligand affinity. ligand affinity and molecular weight. subunit composition and molecular weight. none of these answers are correct. pI and shape.

None of these answers are correct

Which class of protein structures does the protein shown below fit into?

None of these answers are correct

Which of the following statements about association and dissociation constants describing the binding of Ligands X and Y to Protein Z is the most correct?

None of these answers are correct

Choose the best answer below describing why the metabolic cycle discovered by Hans Krebs should be called the citrate cycle is: